package seqAlignment;

public class PairwiseAlignmentRun {
	
	//static String str1="MQRGGDEQ";
	//static String str2="MQRGGGGGDEQ";
	
	//calciumIonProteins
	static String str1="MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK";
	static String str2="MSEEIITPVYCTGVSAQVQKQRARELGLGRHENAIKYLGQDYEQLRVRCLQSGTLFRDEAFPPVPQSLGYKDLGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNDTLLHRVVPHGQSFQNGYAGIFHFQLWQFGEWVDVVVDDLLPIKDGKLVFVHSAEGNEFWSALLEKAYAKVNGSYEALSGGSTSEGFEDFTGGVTEWYELRKAPSDLYQIILKALERGSLLGCSIDISSVLDMEAITFKKLVKGHAYSVTGAKQVNYRGQVVSLIRMRNPWGEVEWTGAWSDSSSEWNNVDPYERDQLRVKMEDGEFWMSFRDFMREFTRLEICNLTPDALKSRTIRKWNTTLYEGTWRRGSTAGGCRNYPATFWVNPQFKIRLDETDDPDDYGDRESGCSFVLALMQKHRRRERRFGRDMETIGFAVYEVPPELVGQPAVHLKRDFFLANASRARSEQFINLREVSTRFRLPPGEYVVVPSTFEPNKEGDFVLRFFSEKSAGTVELDDQIQANLPDEQVLSEEEIDENFKALFRQLAGEDMEISVKELRTILNRIISKHKDLRTKGFSLESCRSMVNLMDRDGNGKLGLVEFNILWNRIRNYLSIFRKFDLDKSGSMSAYEMRMAIESAGFKLNKKLYELIITRYSEPDLAVDFDNFVCCLVRLETMFRFFKTLDTDLDGVVTFDLFKWLQLTMFA";

	//yeastKinaseProteins
	//static String str1="MASLFRPPESAKCNPNSPRLKLPLLRNNQVDENNIYLTSNGSSTTAYSSHTPEPLTSSTSTLFSQTRLHPSDSSMTLNTMKKRPAPPSLPSLSINSQSKCKTLPELVPIADVSDGKHDLGLKQRVIAENELSGNSDLTPSSMASPFSHTNTSSPYLRNDLSNSVGSDFSNLISAYEQSSSPIKSSSQPKSSSESYIDLNSVRDVDQLDENGWKYANLKDRIETLGILGEGAGGSVSKCKLKNGSKIFALKVINTLNTDPEYQKQIFRELQFNRSFQSEYIVRYYGMFTDDENSSIYIAMEYMGGRSLDAIYKNLLERGGRISEKVLGKIAEAVLRGLSYLHEKKVIHRDIKPQNILLNENGQVKLCDFGVSGEAVNSLATTFTGTSFYMAPERIQGQPYSVTSDVWSLGLTILEVANGKFPCSSEKMAANIAPFELLMWILTFTPELKDEPESNIIWSPSFKSFIDYCLKKDSRERPSPRQMINHPWIKGQMKKNVNMEKFVRKCWKD";
	//static String str2="MFQRKTLQRRNLKGLNLNLHPDVGNNGQLQEKTETHQGQSRIEGHVMSNINAIQNNSNLFLRRGIKKKLTLDAFGDDQAISKPNTVVIQQPQNEPVLVLSSLSQSPCVSSSSSLSTPCIIDAYSNNFGLSPSSTNSTPSTIQGLSNIATPVENEHSISLPPLEESLSPAAADLKDTLSGTSNGNYIQLQDLVQLGKIGAGNSGTVVKALHVPDSKIVAKKTIPVEQNNSTIINQLVRELSIVKNVKPHENIITFYGAYYNQHINNEIIILMEYSDCGSLDKILSVYKRFVQRGTVSSKKTWFNELTISKIAYGVLNGLDHLYRQYKIIHRDIKPSNVLINSKGQIKLCDFGVSKKLINSIADTFVGTSTYMSPERIQGNVYSIKGDVWSLGLMIIELVTGEFPLGGHNDTPDGILDLLQRIVNEPSPRLPKDRIYSKEMTDFVNRCCIKNERERSSIHELLHHDLIMKYVSPSKDDKFRHWCRKIKSKIKEDKRIKREALDRAKLEKKQSERSTH";

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		PairwiseAlignmentRun test;
		test = new PairwiseAlignmentRun(str1,str2);
		test.run();
		System.exit(0);
	}
	
	SequenceAlignmentor algntr;
	public PairwiseAlignmentRun(String str1, String str2) {
		algntr=new SequenceAlignmentor(str1, str2);
	}
	
	private void run() {
		algntr.align();
		algntr.output();
		
	}

}
